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| Status |
Public on Sep 01, 2014 |
| Title |
Using RNA sequencing for identifying gene imprinting and random monoallelic expression in human placenta (SNP genotyping) |
| Organism |
Homo sapiens |
| Experiment type |
SNP genotyping by SNP array
Genome variation profiling by SNP array
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| Summary |
Given the possible critical importance of placental gene imprinting and random monoallelic expression on fetal and infant health, most of those genes must be identified, in order to understand the risks that the baby might meet during pregnancy and after birth. Therefore, the aim of the current study was to introduce a workflow and tools for analyzing imprinted and random monoallelic gene expression in human placenta, by applying whole-transcriptome (WT) RNA sequencing of placental tissue and genotyping of coding DNA variants in family trios. Ten family trios, each with a healthy spontaneous single-term pregnancy, were recruited. Total RNA was extracted for WT analysis, providing the full sequence information for the placental transcriptome. Parental and child blood DNA genotypes were analyzed by exome SNP genotyping microarrays, mapping the inheritance and estimating the abundance of parental expressed alleles. Imprinted genes showed consistent expression from either parental allele, as demonstrated by the SNP content of sequenced transcripts, while monoallelically expressed genes had random activity of parental alleles. We revealed 4 novel possible imprinted genes (LGALS8, LGALS14, PAPPA2 and SPTLC3) and confirmed the imprinting of 4 genes (AIM1, PEG10, RHOBTB3 and ZFAT-AS1) in human placenta. The major finding was the identification of 4 genes (ABP1, BCLAF1, IFI30 and ZFAT) with random allelic bias, expressing one of the parental alleles preferentially. The main functions of the imprinted and monoallelically expressed genes included: i) mediating cellular apoptosis and tissue development; ii) regulating inflammation and immune system; iii) facilitating metabolic processes; and iv) regulating cell cycle.
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| Overall design |
Ten family trios (mother, father, child) were analysed using SNP genotyping. Raw data contains additional two samples that were not used.
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| Contributor(s) |
Metsalu T, Viltrop T, Tiirats A, Rajashekar B, Reimann E, Kõks S, Rull K, Milani L, Acharya G, Basnet P, Vilo J, Mägi R, Metspalu A, Peters M, Haller-Kikkatalo K, Salumets A |
| Citation(s) |
25437054 |
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| Submission date |
Apr 10, 2014 |
| Last update date |
Dec 08, 2014 |
| Contact name |
Tauno Metsalu |
| Organization name |
University of Tartu
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| Street address |
Liivi 2
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| City |
Tartu |
| ZIP/Postal code |
50409 |
| Country |
Estonia |
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| Platforms (1) |
| GPL18544 |
Illumina HumanExome-12 v1.0 BeadChip |
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| Samples (30)
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| This SubSeries is part of SuperSeries: |
| GSE56781 |
Using RNA sequencing for identifying gene imprinting and random monoallelic expression in human placenta |
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| Relations |
| BioProject |
PRJNA244577 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE56685_RAW.tar |
25.5 Mb |
(http)(custom) |
TAR |
| GSE56685_geno_matrix_raw.txt.gz |
27.4 Mb |
(ftp)(http) |
TXT |
| Processed data included within Sample table |
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